Function reference • fastTopics

All functions
`compare_fits()`	Summarize and Compare Model Fits
`de_analysis()` `de_analysis_control_default()`	Differential Expression Analysis using a Topic Model
`embedding_plot_2d()` `embedding_plot_2d_ggplot_call()` `pca_plot()` `tsne_plot()` `umap_plot()` `pca_hexbin_plot()` `pca_hexbin_plot_ggplot_call()`	PCA, t-SNE and UMAP Plots
`pca_from_topics()` `tsne_from_topics()` `umap_from_topics()`	Low-dimensional Embeddings from Poisson NMF or Multinomial Topic Model
`fit_multinom_model()`	Fit Simple Multinomial Model
`fit_poisson_nmf()` `fit_poisson_nmf_control_default()` `init_poisson_nmf()` `init_poisson_nmf_from_clustering()`	Fit Non-negative Matrix Factorization to Count Data
`fit_topic_model()`	Simple Interface for Fitting a Multinomial Topic Model
`loglik_poisson_nmf()` `loglik_multinom_topic_model()` `deviance_poisson_nmf()` `cost()`	NMF and Topic Model Likelihoods and Deviances
`loadings_plot()` `loadings_plot_ggplot_call()`	Loadings Plot
`merge_topics()`	Combine Topics in Multinomial Topic Model
`multinom2poisson()`	Recover Poisson NMF Fit from Multinomial Topic Model Fit
`pbmc_facs`	Mixture of 10 FACS-purified PBMC Single-Cell RNA-seq data
`plot_loglik_vs_rank()` `loglik_vs_rank_ggplot_call()`	Plot Log-Likelihood Versus Rank
`plot_progress()`	Plot Progress of Model Fitting Over Time
`poisson2multinom()`	Recover Multinomial Topic Model Fit from Poisson NMF fit
`predict(<poisson_nmf_fit>)` `predict(<multinom_topic_model_fit>)`	Predict Methods for Poisson NMF and Multinomial Topic Model
`run_homer()`	Perform HOMER Motif Enrichment Analysis using DE Genomic Positions
`select(<poisson_nmf_fit>)` `select(<multinom_topic_model_fit>)` `select_loadings()`	Extract or Re-order Data Rows in Poisson NMF or Multinomial Topic Model Fit
`simulate_count_data()`	Simulate Count Data from Poisson NMF Model
`simulate_poisson_gene_data()` `simulate_multinom_gene_data()`	Simulate Gene Expression Data from Poisson NMF or Multinomial Topic Model
`simulate_toy_gene_data()`	Simulate Toy Gene Expression Data
`structure_plot()` `structure_plot_default_embed_method()` `plot(<poisson_nmf_fit>)` `plot(<multinom_topic_model_fit>)` `structure_plot_ggplot_call()`	Structure Plot
`summary(<poisson_nmf_fit>)` `summary(<multinom_topic_model_fit>)` `print(<summary.poisson_nmf_fit>)` `print(<summary.multinom_topic_model_fit>)`	Summarize Poisson NMF or Multinomial Topic Model Fit
`volcano_plot()` `plot(<topic_model_de_analysis>)` `volcano_plotly()` `volcano_plot_do_label_default()` `volcano_plot_ggplot_call()` `volcano_plot_ly_call()`	Volcano Plots for Visualizing Results of Differential Expression Analysis

Reference

All functions